I have a list of around 300 protein PDB IDs, and I want to identify structural motifs in the set of proteins by finding the structural motifs that are in common between the proteins in the set. I want it to predict motifs using 3D structure, not primarily through sequence motifs.

I tried DALI, but DALI only works for up to 64 proteins (unless there's a workaround for that?). I was also trying MASS, but the web server is down now, although the tool seems to be quite useful for what I'm trying to do (Linux is also being a pain on my computer right now). Any help would be greatly appreciated!